Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation

Cell. 2019 Apr 4;177(2):446-462.e16. doi: 10.1016/j.cell.2019.03.024.


Poor reproducibility within and across studies arising from lack of knowledge regarding the performance of extracellular RNA (exRNA) isolation methods has hindered progress in the exRNA field. A systematic comparison of 10 exRNA isolation methods across 5 biofluids revealed marked differences in the complexity and reproducibility of the resulting small RNA-seq profiles. The relative efficiency with which each method accessed different exRNA carrier subclasses was determined by estimating the proportions of extracellular vesicle (EV)-, ribonucleoprotein (RNP)-, and high-density lipoprotein (HDL)-specific miRNA signatures in each profile. An interactive web-based application (miRDaR) was developed to help investigators select the optimal exRNA isolation method for their studies. miRDar provides comparative statistics for all expressed miRNAs or a selected subset of miRNAs in the desired biofluid for each exRNA isolation method and returns a ranked list of exRNA isolation methods prioritized by complexity, expression level, and reproducibility. These results will improve reproducibility and stimulate further progress in exRNA biomarker development.

Keywords: extracellular RNA; extracellular vesicles; lipoprotein; ribonucleoprotein.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Body Fluids / chemistry
  • Cell Line
  • Cell-Free Nucleic Acids / isolation & purification*
  • Circulating MicroRNA / isolation & purification*
  • Extracellular Vesicles / metabolism
  • Female
  • Healthy Volunteers
  • Humans
  • Male
  • MicroRNAs / isolation & purification
  • MicroRNAs / metabolism
  • RNA / isolation & purification*
  • RNA / metabolism
  • Reproducibility of Results
  • Sequence Analysis, RNA / methods


  • Cell-Free Nucleic Acids
  • Circulating MicroRNA
  • MicroRNAs
  • RNA